measurePsf.py

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#
# LSST Data Management System
# Copyright 2008, 2009, 2010, 2011 LSST Corporation.
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import lsst.afw.math as afwMath
import lsst.afw.display.ds9 as ds9
import lsst.meas.algorithms as measAlg
import lsst.meas.algorithms.utils as maUtils
import lsst.pex.config as pexConfig
import lsst.pipe.base as pipeBase
import lsst.afw.table as afwTable

class MeasurePsfConfig(pexConfig.Config):
    starSelector = measAlg.starSelectorRegistry.makeField("Star selection algorithm", default="secondMoment")
    psfDeterminer = measAlg.psfDeterminerRegistry.makeField("PSF Determination algorithm", default="pca")

## \addtogroup LSST_task_documentation
## \{
## \page MeasurePsfTask
## \ref MeasurePsfTask_ "MeasurePsfTask"
## \copybrief MeasurePsfTask
## \}

class MeasurePsfTask(pipeBase.Task):
    """!
\anchor MeasurePsfTask_

\brief Measure the PSF

\section pipe_tasks_measurePsf_Contents Contents

 - \ref pipe_tasks_measurePsf_Purpose
 - \ref pipe_tasks_measurePsf_Initialize
 - \ref pipe_tasks_measurePsf_IO
 - \ref pipe_tasks_measurePsf_Config
 - \ref pipe_tasks_measurePsf_Debug
 - \ref pipe_tasks_measurePsf_Example

\section pipe_tasks_measurePsf_Purpose  Description

\copybrief MeasurePsfTask


A task that wraps two algorithms set via a pair of registries specified in the task's
\ref pipe_tasks_measurePsf_Config.
Both algorithms are classes with a constructor taking a pex.config.Config object (\em e.g.
lsst.meas.algorithms.objectSizeStarSelector.ObjectSizeStarSelector.__init__).

The algorithms are:
 - a star selector with API:
\code
selectStars(self, exposure, catalog, matches=None)
\endcode
which returns a list of lsst.meas.algorithms.PsfCandidate (\em e.g.
lsst.meas.algorithms.objectSizeStarSelector.ObjectSizeStarSelector.selectStars)

 - a psf estimator with API:
\code
determinePsf(exposure, psfCandidateList, metadata=None, flagKey=None)
\endcode
which returns an lsst.afw.detection.Psf and lsst.afw.math.SpatialCellSet (\em e.g.
lsst.meas.algorithms.pcaPsfDeterminer.PcaPsfDeterminer.determinePsf).
MeasurePsfTask calls determinePsf with \c flagKey set to
"calib.psf.used" if a schema is passed to its constructor (see \ref pipe_tasks_measurePsf_Initialize).

See also lsst.meas.algorithms.starSelectorRegistry.starSelectorRegistry and
lsst.meas.algorithms.psfDeterminerRegistry.psfDeterminerRegistry.

\warning
There is no establised set of configuration parameters for these algorithms, so once you start modifying
parameters (as we do in \ref pipe_tasks_measurePsf_Example) your code is no longer portable.

\section pipe_tasks_measurePsf_Initialize       Task initialisation

\copydoc \_\_init\_\_

\section pipe_tasks_measurePsf_IO               Invoking the Task

\copydoc run

\section pipe_tasks_measurePsf_Config       Configuration parameters

See \ref MeasurePsfConfig

\warning
The star selector and psf determiner registries should be modified to return a class
which has a ConfigClass attribute and can be instantiated with a config. Until then, there's no
obvious way to get a registry algorithm's Config from another Config.

\section pipe_tasks_measurePsf_Debug            Debug variables

The \link lsst.pipe.base.cmdLineTask.CmdLineTask command line task\endlink interface supports a
flag \c -d to import \b debug.py from your \c PYTHONPATH; see \ref baseDebug for more about \b debug.py files.

<DL>
  <DT> \c display
  <DD> If True, display debugging plots
  <DT> displayExposure
  <DD> display the Exposure + spatialCells
  <DT> displayPsfCandidates
  <DD> show mosaic of candidates
  <DT> showBadCandidates
  <DD> Include bad candidates
  <DT> displayPsfMosaic
  <DD> show mosaic of reconstructed PSF(xy)
  <DT> displayResiduals
  <DD> show residuals
  <DT> normalizeResiduals
  <DD> Normalise residuals by object amplitude
</DL>

Additionally you can enable any debug outputs that your chosen star selector and psf determiner support.

\section pipe_tasks_measurePsf_Example  A complete example of using MeasurePsfTask

This code is in \link measurePsfTask.py\endlink in the examples directory, and can be run as \em e.g.
\code
examples/measurePsfTask.py --ds9
\endcode
\dontinclude measurePsfTask.py
The example also runs SourceDetectionTask and SourceMeasurementTask; see \ref meas_algorithms_measurement_Example for more explanation.

Import the tasks (there are some other standard imports; read the file to see them all)
\skip SourceDetectionTask
\until MeasurePsfTask

We need to create the tasks before processing any data as the task constructor
can add an extra column to the schema, but first we need an almost-empty Schema
\skipline makeMinimalSchema
after which we can call the constructors for the tasks we need to find and characterize candidate
PSF stars:
\skip SourceDetectionTask.ConfigClass
\until measureTask
Now the task that we're interested in:
\skipline MeasurePsfTask.ConfigClass
\skipline MeasurePsfTask

Unfortunately that won't quite work as we didn't run the standard bright star measuring code
which sets fields such as "initial.flags.pixel.edge" rather than "flags.pixel.edge".  One option
would have been to modify the SourceMeasurementTask configuration with
\code
config.prefix = "initial."
config.algorithms.names -= ["correctfluxes"]
\endcode
(you need the second line due to a bug present in the aperture correction code as of 2014-07-01);
or we can set \c badFlags
\dontinclude measurePsfTask.py
\skip starSelector
\until flags.pixel.saturated.center
(not beautiful)

We can set psfDeterminer options too:
\skip psfDeterminer
\until nEigenComponents

before creating our task
\skipline MeasurePsfTask

We're now ready to process the data (we could loop over multiple exposures/catalogues using the same
task objects).  First create the output table:
\skipline afwTable

And process the image
\skip sources =
\until result

We can then unpack and use the results:
\skip psf
\until cellSet
If you specified \c --ds9 you can see the PSF candidates:
\skip display
\until RED

<HR>
To investigate the \ref pipe_tasks_measurePsf_Debug, put something like
\code{.py}
    import lsstDebug
    def DebugInfo(name):
        di = lsstDebug.getInfo(name)        # N.b. lsstDebug.Info(name) would call us recursively

        if name == "lsst.pipe.tasks.measurePsf" :
            di.display = True
            di.displayExposure = False          # display the Exposure + spatialCells
            di.displayPsfCandidates = True      # show mosaic of candidates
            di.displayPsfMosaic = True          # show mosaic of reconstructed PSF(xy)
            di.displayResiduals = True          # show residuals
            di.showBadCandidates = True         # Include bad candidates
            di.normalizeResiduals = False       # Normalise residuals by object amplitude

        return di

    lsstDebug.Info = DebugInfo
\endcode
into your debug.py file and run measurePsfTask.py with the \c --debug flag.
    """
    ConfigClass = MeasurePsfConfig
    _DefaultName = "measurePsf"

    def __init__(self, schema=None, **kwargs):
        """!Create the detection task.  Most arguments are simply passed onto pipe.base.Task.

        \param schema An lsst::afw::table::Schema used to create the output lsst.afw.table.SourceCatalog
        \param **kwargs Keyword arguments passed to lsst.pipe.base.task.Task.__init__.

        If schema is not None, 'calib.psf.candidate' and 'calib.psf.used' fields will be added to
        identify which stars were employed in the PSF estimation.

        \note This task can add fields to the schema, so any code calling this task must ensure that
        these fields are indeed present in the input table.
        """

        pipeBase.Task.__init__(self, **kwargs)
        if schema is not None:
            if schema.getVersion() == 0:
                self.candidateKey = schema.addField(
                    "calib.psf.candidate", type="Flag",
                    doc=("Flag set if the source was a candidate for PSF determination, "
                         "as determined by the '%s' star selector.") % self.config.starSelector.name
                    )
                self.usedKey = schema.addField(
                    "calib.psf.used", type="Flag",
                    doc=("Flag set if the source was actually used for PSF determination, "
                         "as determined by the '%s' PSF determiner.") % self.config.psfDeterminer.name
                    )
            else:
                self.candidateKey = schema.addField(
                    "calib_psfCandidate", type="Flag",
                    doc=("Flag set if the source was a candidate for PSF determination, "
                         "as determined by the '%s' star selector.") % self.config.starSelector.name
                    )
                self.usedKey = schema.addField(
                    "calib_psfUsed", type="Flag",
                    doc=("Flag set if the source was actually used for PSF determination, "
                         "as determined by the '%s' PSF determiner.") % self.config.psfDeterminer.name
                    )
        else:
            self.candidateKey = None
            self.usedKey = None
        self.starSelector = self.config.starSelector.apply()
        self.psfDeterminer = self.config.psfDeterminer.apply()

    @pipeBase.timeMethod
    def run(self, exposure, sources, matches=None):
        """!Measure the PSF

        \param[in,out]   exposure      Exposure to process; measured PSF will be added.
        \param[in,out]   sources       Measured sources on exposure; flag fields will be set marking
                                       stars chosen by the star selector and the PSF determiner if a schema
                                       was passed to the task constructor.

        \param[in] matches a list of lsst.afw.table.ReferenceMatch objects (\em i.e. of lsst.afw.table.Match
                                       with \c first being of type lsst.afw.table.SimpleRecord and \c second
                                       type lsst.afw.table.SourceRecord --- the reference object and detected
                                       object respectively) as returned by \em e.g. the AstrometryTask.
                                       Used by star selectors that choose to refer to an external catalog.

        \return a pipe.base.Struct with fields:
         - psf: The measured PSF (also set in the input exposure)
         - cellSet: an lsst.afw.math.SpatialCellSet containing the PSF candidates as returned by the psf determiner.
        """
        self.log.info("Measuring PSF")

        import lsstDebug
        display = lsstDebug.Info(__name__).display
        displayExposure = lsstDebug.Info(__name__).displayExposure     # display the Exposure + spatialCells
        displayPsfMosaic = lsstDebug.Info(__name__).displayPsfMosaic # show mosaic of reconstructed PSF(x,y)
        displayPsfCandidates = lsstDebug.Info(__name__).displayPsfCandidates # show mosaic of candidates
        displayResiduals = lsstDebug.Info(__name__).displayResiduals   # show residuals
        showBadCandidates = lsstDebug.Info(__name__).showBadCandidates # include bad candidates
        normalizeResiduals = lsstDebug.Info(__name__).normalizeResiduals # normalise residuals by object peak

        #-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
        #
        # Run star selector
        #
        psfCandidateList = self.starSelector.selectStars(exposure, sources, matches=matches)
        if psfCandidateList and self.candidateKey is not None:
            for cand in psfCandidateList:
                source = cand.getSource()
                source.set(self.candidateKey, True)

        self.log.info("PSF star selector found %d candidates" % len(psfCandidateList))

        if display:
            frame = display
            if displayExposure:
                ds9.mtv(exposure, frame=frame, title="psf determination")

        #-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
        #
        # Determine PSF
        #
        psf, cellSet = self.psfDeterminer.determinePsf(exposure, psfCandidateList, self.metadata,
                                                       flagKey=self.usedKey)
        self.log.info("PSF determination using %d/%d stars." %
                     (self.metadata.get("numGoodStars"), self.metadata.get("numAvailStars")))

        exposure.setPsf(psf)

        if display:
            frame = display
            if displayExposure:
                showPsfSpatialCells(exposure, cellSet, showBadCandidates, frame=frame)
                frame += 1

            if displayPsfCandidates:    # Show a mosaic of  PSF candidates
                plotPsfCandidates(cellSet, showBadCandidates, frame)
                frame += 1

            if displayResiduals:
                frame = plotResiduals(exposure, cellSet,
                                      showBadCandidates=showBadCandidates,
                                      normalizeResiduals=normalizeResiduals,
                                      frame=frame)
            if displayPsfMosaic:
                maUtils.showPsfMosaic(exposure, psf, frame=frame, showFwhm=True)
                ds9.scale(0, 1, "linear", frame=frame)
                frame += 1

        return pipeBase.Struct(
            psf = psf,
            cellSet = cellSet,
        )

#-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
#
# Debug code
#
def showPsfSpatialCells(exposure, cellSet, showBadCandidates, frame=1):
    maUtils.showPsfSpatialCells(exposure, cellSet,
                                symb="o", ctype=ds9.CYAN, ctypeUnused=ds9.YELLOW,
                                size=4, frame=frame)
    for cell in cellSet.getCellList():
        for cand in cell.begin(not showBadCandidates): # maybe include bad candidates
            cand = measAlg.cast_PsfCandidateF(cand)
            status = cand.getStatus()
            ds9.dot('+', *cand.getSource().getCentroid(), frame=frame,
                    ctype=ds9.GREEN if status == afwMath.SpatialCellCandidate.GOOD else
                    ds9.YELLOW if status == afwMath.SpatialCellCandidate.UNKNOWN else ds9.RED)

def plotPsfCandidates(cellSet, showBadCandidates=False, frame=1):
    import lsst.afw.display.utils as displayUtils

    stamps = []
    for cell in cellSet.getCellList():
        for cand in cell.begin(not showBadCandidates): # maybe include bad candidates
            cand = measAlg.cast_PsfCandidateF(cand)

            try:
                im = cand.getMaskedImage()

                chi2 = cand.getChi2()
                if chi2 < 1e100:
                    chi2 = "%.1f" % chi2
                else:
                    chi2 = numpy.nan

                stamps.append((im, "%d%s" %
                               (maUtils.splitId(cand.getSource().getId(), True)["objId"], chi2),
                               cand.getStatus()))
            except Exception, e:
                continue

    mos = displayUtils.Mosaic()
    for im, label, status in stamps:
        im = type(im)(im, True)
        try:
            im /= afwMath.makeStatistics(im, afwMath.MAX).getValue()
        except NotImplementedError:
            pass

        mos.append(im, label,
                   ds9.GREEN if status == afwMath.SpatialCellCandidate.GOOD else
                   ds9.YELLOW if status == afwMath.SpatialCellCandidate.UNKNOWN else ds9.RED)

    if mos.images:
        mos.makeMosaic(frame=frame, title="Psf Candidates")

def plotResiduals(exposure, cellSet, showBadCandidates=False, normalizeResiduals=True, frame=2):
    psf = exposure.getPsf()
    while True:
        try:
            maUtils.showPsfCandidates(exposure, cellSet, psf=psf, frame=frame,
                                      normalize=normalizeResiduals,
                                      showBadCandidates=showBadCandidates)
            frame += 1
            maUtils.showPsfCandidates(exposure, cellSet, psf=psf, frame=frame,
                                      normalize=normalizeResiduals,
                                      showBadCandidates=showBadCandidates,
                                      variance=True)
            frame += 1
        except Exception as e:
            if not showBadCandidates:
                showBadCandidates = True
                continue
        break

    return frame